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Sodium in PDB 4hdb: Crystal Structure of Hiv-1 Protease Mutants D30N Complexed with Inhibitor Grl-0519

Enzymatic activity of Crystal Structure of Hiv-1 Protease Mutants D30N Complexed with Inhibitor Grl-0519

All present enzymatic activity of Crystal Structure of Hiv-1 Protease Mutants D30N Complexed with Inhibitor Grl-0519:
3.4.23.16;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Protease Mutants D30N Complexed with Inhibitor Grl-0519, PDB code: 4hdb was solved by H.Zhang, Y.-F.Wang, C.H.Shen, J.Agniswamy, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.49
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.723, 86.243, 45.898, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 21.4

Other elements in 4hdb:

The structure of Crystal Structure of Hiv-1 Protease Mutants D30N Complexed with Inhibitor Grl-0519 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Hiv-1 Protease Mutants D30N Complexed with Inhibitor Grl-0519 (pdb code 4hdb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Hiv-1 Protease Mutants D30N Complexed with Inhibitor Grl-0519, PDB code: 4hdb:

Sodium binding site 1 out of 1 in 4hdb

Go back to Sodium Binding Sites List in 4hdb
Sodium binding site 1 out of 1 in the Crystal Structure of Hiv-1 Protease Mutants D30N Complexed with Inhibitor Grl-0519


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Hiv-1 Protease Mutants D30N Complexed with Inhibitor Grl-0519 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:23.1
occ:1.00
 O A:HOH1006 2.2 25.8 1.0
O A:HOH1005 2.3 21.6 1.0
O A:ASP60 2.3 16.8 1.0
O A:HOH1004 2.4 22.1 1.0
O A:HOH1007 2.5 35.3 1.0
O A:HOH1003 2.9 30.2 1.0
C A:ASP60 3.4 15.6 1.0
N A:ASP60 3.7 13.4 1.0
CA A:ASP60 4.0 15.4 1.0
O A:HOH1058 4.1 32.0 0.5
O A:ARG41 4.2 20.6 1.0
CB A:ASP60 4.4 16.4 1.0
N A:GLN61 4.4 14.5 1.0
CB A:GLN61 4.5 19.2 1.0
N A:ARG41 4.5 23.1 1.0
CD1 A:ILE62 4.5 18.9 1.0
O A:GLN61 4.6 19.4 1.0
O A:HOH1008 4.7 38.8 1.0
O A:PRO39 4.7 22.4 1.0
C A:TYR59 4.7 12.0 1.0
C A:GLN61 4.8 15.1 1.0
CA A:GLN61 4.8 15.0 1.0
O A:HOH1091 4.8 25.6 0.5
CA A:GLY40 4.9 24.2 1.0

Reference:

H.Zhang, Y.F.Wang, C.H.Shen, J.Agniswamy, K.V.Rao, C.X.Xu, A.K.Ghosh, R.W.Harrison, I.T.Weber. Novel P2 Tris-Tetrahydrofuran Group in Antiviral Compound 1 (Grl-0519) Fills the S2 Binding Pocket of Selected Mutants of Hiv-1 Protease. J.Med.Chem. V. 56 1074 2013.
ISSN: ISSN 0022-2623
PubMed: 23298236
DOI: 10.1021/JM301519Z
Page generated: Sun Aug 17 19:38:28 2025

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